User GuidesSnapGene User Guide SearchingSearch for a Protein Sequence

Search for a Protein Sequence

How do I search for a protein sequence?

Show the Find Controls

To show the Find controls, click Edit Find Find Protein Sequence.  

The Find controls will appear near the bottom of the window and Find protein sequence will be selected.

Show Translations (Optional)

A protein sequence search is restricted to visible translations, which are typically present in translated features. If you also wish to show full-sequence translations, click the Show Translations button.

Enter the Protein Sequence

Enter the protein sequence you wish to search for in the search box, then click Next.

Search with Ambiguous Amino Acids

To allow any amino acids at a specific position, use X.

Search with Excluded Amino Acids

To exclude amino acids at a particular position, use an exclamation point in front of the forbidden amino acids. For example, !P means not P.

Alternatively, enclose the excluded amino acids in parentheses. For example, !(ST) means not S or T.

Search for a Degenerate Amino Acid

To search for a degenerate amino acid, enclose the entire query in quotes. For example, a search for X will find all matches to any letter (A-Z), but a search for "X" will find only bases actually represented as X.

The other degenerate amino acids are B (matching either D or N) and Z (matching either E or Q).

Review Recent Searches

To review or reuse recent searches, click the arrow button on the search box.

See the Matches in Map View

In Map view, a matching protein sequence will be highlighted in blue.

See the Matches in Sequence View

In Sequence view, a matching protein sequence will be highlighted in blue.

Show the Search Tips

To view examples of protein searches, click Help → Search Tips, then scroll down.

Alternatively, choose Search Tips from the Find controls.

View the Protein Letter Codes

To view a list of protein letter codes, click Tools → Letter Codes, then click the triangle next to Protein Letter Codes.